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ECOGEMS

ECOGEMS

ECOGEMS is a tool to compress into sparse matrices and retrieve SNP data for rice. ECOGEMS has a graphical interface for visualization and downloading SNP data.

Topic

Genetic variation; DNA polymorphism; Database management; Model organisms

Details

  • Operation: Query and retrieval
  • Software interface: Command-line user interface; web user interface
  • Language: R
  • Operating system: Microsoft Windows, Mac OS X, Linux
  • License: Not stated
  • Cost: Free
  • Version name: -
  • Maturity: Emerging
  • Credit: The key grant science and technique foundation of Henan province, the research start-up fund to top notch talents of Henan Agricultural University.
  • Contact: Jihua Tan tangjihua1 _at_ 163.com | Wen Yao yaowen _at_ henau.edu.cn
  • Collection: -

Publications

Yao W, Huang F, Zhang X, Tang J "ECOGEMS: efficient compression and retrieve of SNP data of 2058 rice accessions with integer sparse matrices." Bioinformatics. 2019 Oct 15;35(20):4181-4183. https://doi.org/10.1093/bioinformatics/btz186
PMID: 30873546


Download and documentation




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